debian/changelog

+htsjdk (2.16.1+dfsg-2) unstable; urgency=medium
+
+  * Fix FTBS with OpenJDK 11 (Closes: #913566) 
+
+ -- Olivier Sallou <osallou@debian.org>  Mon, 12 Nov 2018 15:38:32 +0000
+
 htsjdk (2.16.1+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]

debian/control

@@ -13,6 +13,8 @@ Build-Depends: default-jdk (>= 2:1.9),
                debhelper (>= 11~),
                libcommons-jexl2-java,
                libcommons-logging-java,
+               libjaxb-api-java,
+               libjaxb-java,
                libsnappy-java,
                libcommons-compress-java,
                libxz-java (>= 1.5),

debian/libhtsjdk-java.classpath

-usr/share/java/htsjdk.jar /usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/snappy-java.jar /usr/share/java/commons-compress.jar /usr/share/java/xz.jar /usr/share/java/ngs-java.jar
+usr/share/java/htsjdk.jar /usr/share/java/commons-jexl2.jar /usr/share/java/commons-logging.jar /usr/share/java/snappy-java.jar /usr/share/java/commons-compress.jar /usr/share/java/xz.jar /usr/share/java/ngs-java.jar /usr/share/java/libjaxb-api.jar /usr/share/java/jaxb-impl.jar

debian/patches/100-fix-java11

+Subject: add jaxb-api jar for openjdk 11
+Description: xml.bind has been removed from openjdk 11,
+ add jaxb-api jar file to compilation and classpath
+Author: Olivier Sallou <osallou@debian.org>
+Last-Updated: 2018-11-12
+Forwarded: no
+--- a/build.gradle
++++ b/build.gradle
+@@ -22,12 +22,14 @@
+     compile "org.apache.commons:commons-compress:1.4.1"
+     compile "org.tukaani:xz:1.5"
+     compile "gov.nih.nlm.ncbi:ngs-java:2.9.0"
++    compile "javax.xml.bind:jaxb-api:debian"
+ 
+     testCompile "org.scala-lang:scala-library:2.11.x"
+     //testCompile "org.scalatest:scalatest_2.12:3.0.5"
+     //testRuntime 'org.pegdown:pegdown:1.6.0' // Necessary for generating HTML reports with ScalaTest
+     testCompile "org.testng:testng:debian"
+     testCompile "com.google.jimfs:jimfs:debian"
++    testCompile "com.sun.xml.bind:jaxb-impl:debian"
+  }
+ 
+ sourceCompatibility = 1.8
+@@ -93,7 +95,6 @@
+     if (System.env.CI == "true") {
+         jvmArgs += '-Dsamjdk.sra_libraries_download=true'
+     }
+-    jvmArgs += ["--add-modules", "java.xml.bind"]
+ 
+     exclude 'htsjdk/samtools/sra/**'
+     exclude 'htsjdk/samtools/BAMFileIndexTest.java'
+@@ -120,7 +121,6 @@
+ if (JavaVersion.current().isJava8Compatible()) {
+     tasks.withType(Javadoc) {
+         options.addStringOption('Xdoclint:none', '-quiet')
+-        options.addStringOption('-add-modules', 'java.xml.bind')
+     }
+ }
+ 

debian/patches/series

@@ -9,3 +9,4 @@
 80-2to3.patch
 90-disable-testftp.patch
 92-disable-testhttp.patch
+100-fix-java11